X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 292.0
Details 3.0 M ammonium sulfate, 0.1 M HEPES pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.64 α = 90
b = 115.05 β = 90
c = 39.37 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-10-19
Diffraction Radiation
Monochromator Protocol
Si - 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.9 25 99.8 0.062 -- -- -- -- 17741 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.9 2.0 100.0 0.558 -- -- 5.3 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
PDB ID 1DKZ 1.9 25.0 -- -- -- 16807 901 99.57 -- 0.22064 0.21776 0.27582 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.9 1.949 -- 55 1136 0.272 0.383 -- 99.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.847
Anisotropic B[1][1] -0.88
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 16.106
r_dihedral_angle_4_deg 16.033
r_gen_planes_refined 0.01
r_dihedral_angle_1_deg 5.227
r_chiral_restr 0.129
r_bond_refined_d 0.017
r_dihedral_angle_2_deg 42.028
r_angle_refined_deg 1.931
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1749
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 80

Software

Software
Software Name Purpose
marccd data collection
REFMAC refinement version: with PDBID 1DKZ
XDS data reduction
SCALA data scaling
REFMAC phasing version: with PDBID 1DKZ